GapMind for catabolism of small carbon sources

 

Protein GFF3785 in Pseudomonas stutzeri RCH2

Annotation: FitnessBrowser__psRCH2:GFF3785

Length: 234 amino acids

Source: psRCH2 in FitnessBrowser

Candidate for 20 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-isoleucine catabolism livF hi High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 44% 92% 183 ABC branched-chain amino acid transporter, ATP-binding component, component of Uptake transporter, CamABCD of cholate (steroid) metabolites, 1β(2'-propanoate)-3aα-H-4α(3"(R)-hydroxy-3"-propanoate)-7aβ-methylhexahydro-5-indanone and a desaturated analog 42% 172.6
L-leucine catabolism livF hi High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 44% 92% 183 ABC branched-chain amino acid transporter, ATP-binding component, component of Uptake transporter, CamABCD of cholate (steroid) metabolites, 1β(2'-propanoate)-3aα-H-4α(3"(R)-hydroxy-3"-propanoate)-7aβ-methylhexahydro-5-indanone and a desaturated analog 42% 172.6
L-valine catabolism livF hi High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 44% 92% 183 ABC branched-chain amino acid transporter, ATP-binding component, component of Uptake transporter, CamABCD of cholate (steroid) metabolites, 1β(2'-propanoate)-3aα-H-4α(3"(R)-hydroxy-3"-propanoate)-7aβ-methylhexahydro-5-indanone and a desaturated analog 42% 172.6
L-alanine catabolism braG med High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 44% 92% 183 high-affinity branched-chain amino acid ABC transporter, ATP-binding protein LivF 44% 181.0
L-serine catabolism braG med High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 44% 92% 183 high-affinity branched-chain amino acid ABC transporter, ATP-binding protein LivF 44% 181.0
L-threonine catabolism braG med High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 44% 92% 183 high-affinity branched-chain amino acid ABC transporter, ATP-binding protein LivF 44% 181.0
L-phenylalanine catabolism livF med high-affinity branched-chain amino acid ABC transporter, ATP-binding protein LivF (characterized) 44% 97% 181 ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM 42% 177.6
L-arginine catabolism braG med ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 44% 88% 166.4 High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine 44% 183.0
L-glutamate catabolism braG med ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 44% 88% 166.4 High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine 44% 183.0
L-histidine catabolism braG med ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 44% 88% 166.4 High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine 44% 183.0
L-proline catabolism HSERO_RS00900 med ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale) 42% 90% 166 High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine 44% 183.0
D-alanine catabolism AZOBR_RS08250 med Leucine//isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale) 42% 90% 164.1 High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine 44% 183.0
L-proline catabolism AZOBR_RS08250 med Leucine//isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale) 42% 90% 164.1 High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine 44% 183.0
L-serine catabolism Ac3H11_1692 med ABC transporter ATP-binding protein (characterized, see rationale) 42% 88% 162.2 High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine 44% 183.0
L-tyrosine catabolism Ac3H11_1692 med ABC transporter ATP-binding protein (characterized, see rationale) 42% 88% 162.2 High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine 44% 183.0
L-isoleucine catabolism natE lo NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) 38% 85% 152.9 High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine 44% 183.0
L-leucine catabolism natE lo NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) 38% 85% 152.9 High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine 44% 183.0
L-proline catabolism natE lo NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) 38% 85% 152.9 High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine 44% 183.0
L-valine catabolism natE lo NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) 38% 85% 152.9 High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine 44% 183.0
L-arabinose catabolism xylGsa lo Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale) 32% 96% 117.5 High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine 44% 183.0

Sequence Analysis Tools

View GFF3785 at FitnessBrowser

Find papers: PaperBLAST

Find functional residues: SitesBLAST

Search for conserved domains

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Compare to protein structures

Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

Find homologs in fast.genomics

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Sequence

MTEPLLSVRDLNAWYGESHALHGIDLDVHAGETVTLLGRNGVGKTTALRAIVGIIRKRSG
SIRFDGKDMLRVPLHRTARHGIGYVPEERGIFSTLTVEENLTLPPVVAKGGMTLAEIYQL
FPNLEERRKSPGTKLSGGEQQMLAMARILRTGAKLLLLDEPTEGLAPVIIQRIGEVLQTL
KQRGMTILLVEQNFRFASKVADRFYVVDHGQVIDHFAVDELPDRMSMLNEALGV

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory